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1 import unittest
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2 from commons.launcher.MafftProgramLauncher import MafftProgramLauncher
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3
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4 class Test_MafftProgramLauncher( unittest.TestCase ):
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5
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6
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7 def setUp( self ):
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8 self._i = MafftProgramLauncher()
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9
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10
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11 def tearDown( self ):
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12 self._i = None
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13
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14
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15 def test_getSpecificHelpAsString( self ):
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16 exp = ""
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17 exp += "\nspecific options:"
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18 exp += "\n -p: parameters for '%s' (default='--auto')" % ( "mafft" )
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19 exp += "\n -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln')"
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20 obs = self._i.getSpecificHelpAsString()
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21 self.assertEqual( exp, obs )
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22
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23
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24 def test_setASpecificAttributeFromCmdLine( self ):
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25 self._i.setASpecificAttributeFromCmdLine( "-p", "'--auto --maxiterate 500'" )
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26 self.assertEqual( "'--auto --maxiterate 500'", self._i.getProgramParameters() )
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27
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28 self._i.setASpecificAttributeFromCmdLine( "-o", "dummyOutFile.fa_aln" )
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29 self.assertEqual( "dummyOutFile.fa_aln", self._i.getOutputFile() )
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30
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31
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32 def test_setWrapperCommandLine( self ):
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33 inFile = "dummyInFile.fa"
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34 self._i.setInputFile( inFile )
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35 exp = "MafftProgramLauncher.py"
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36 exp += " -i %s" % ( inFile )
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37 exp += " -p '%s'" % ( "--auto" )
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38 exp += " -o %s.fa_aln" % ( inFile )
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39 exp += " -v 0"
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40 self._i.setWrapperCommandLine()
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41 obs = self._i.getWrapperCommandLine()
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42 self.assertEqual( exp, obs )
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43
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44
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45 def test_setProgramCommandLine( self ):
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46 inFile = "dummyInFile.fa"
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47 self._i.setInputFile( inFile )
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48 exp = self._i.getProgramName()
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49 exp += " %s" % ( "--auto" )
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50 exp += " --quiet"
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51 exp += " %s.shortH" % ( inFile )
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52 exp += " > %s.shortH.fa_aln" % ( inFile )
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53 exp += " 2> /dev/null"
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54 self._i.setProgramCommandLine()
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55 obs = self._i.getProgramCommandLine()
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56 self.assertEqual( exp, obs )
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57
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58
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59 def test_setListFilesToKeep( self ):
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60 inFile = "dummyInFile.fa"
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61 self._i.setInputFile( inFile )
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62 self._i.setListFilesToKeep()
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63 lExp = [ "dummyInFile.fa.fa_aln" ]
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64 lObs = self._i.getListFilesToKeep()
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65 lExp.sort()
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66 lObs.sort()
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67 self.assertEqual( lExp, lObs )
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68
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69 self._i._lFilesToKeep = []
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70
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71 outFile = "dummyOutFile.fa_aln"
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72 self._i.setOutputFile( outFile )
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73 self._i.setListFilesToKeep()
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74 lExp = [ outFile ]
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75 lObs = self._i.getListFilesToKeep()
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76 lExp.sort()
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77 lObs.sort()
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78 self.assertEqual( lExp, lObs )
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79
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80
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81 def test_setListFilesToRemove( self ):
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82 inFile = "dummyInFile.fa"
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83 self._i.setInputFile( inFile )
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84 self._i.setListFilesToRemove()
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85 lExp = [ "dummyInFile.fa.shortH", \
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86 "dummyInFile.fa.shortH.fa_aln", \
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87 "dummyInFile.fa.shortHlink" ]
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88 lObs = self._i.getListFilesToRemove()
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89 lExp.sort()
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90 lObs.sort()
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91 self.assertEqual( lExp, lObs )
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92
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93
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94 def test_setSummary( self ):
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95 self._i.setInputFile( "dummyInFile.fa" )
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96 exp = "input file: %s" % ( "dummyInFile.fa" )
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97 exp += "\nparameters: %s" % ( "--auto" )
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98 exp += "\noutput file: %s" % ( "dummyInFile.fa.fa_aln" )
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99 self._i.setSummary()
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100 obs = self._i.getSummary()
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101 self.assertEqual( exp, obs )
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102
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103
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104 if __name__ == "__main__":
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105 unittest.main() |
